Starting phenix.real_space_refine on Fri Dec 27 07:19:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wed_32447/12_2024/7wed_32447.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wed_32447/12_2024/7wed_32447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wed_32447/12_2024/7wed_32447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wed_32447/12_2024/7wed_32447.map" model { file = "/net/cci-nas-00/data/ceres_data/7wed_32447/12_2024/7wed_32447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wed_32447/12_2024/7wed_32447.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2132 2.51 5 N 572 2.21 5 O 638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3358 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.99, per 1000 atoms: 0.89 Number of scatterers: 3358 At special positions: 0 Unit cell: (110.21, 72.76, 72.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 638 8.00 N 572 7.00 C 2132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 371.4 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 8.4% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.570A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 390 removed outlier: 4.403A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.400A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'H' and resid 63 through 66 removed outlier: 3.749A pdb=" N GLN H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 66' Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.234A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.789A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.620A pdb=" N THR H 118 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU H 35 " --> pdb=" O TRP H 51 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRP H 51 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP H 51 " --> pdb=" O ASN H 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.620A pdb=" N THR H 118 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.284A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR L 103 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER L 54 " --> pdb=" O SER L 50 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1076 1.35 - 1.47: 922 1.47 - 1.59: 1429 1.59 - 1.71: 0 1.71 - 1.83: 18 Bond restraints: 3445 Sorted by residual: bond pdb=" C SER L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 3.99e+00 bond pdb=" C CYS E 432 " pdb=" N VAL E 433 " ideal model delta sigma weight residual 1.331 1.348 -0.017 1.50e-02 4.44e+03 1.33e+00 bond pdb=" CB ARG H 42 " pdb=" CG ARG H 42 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C ASN E 331 " pdb=" N ILE E 332 " ideal model delta sigma weight residual 1.329 1.344 -0.015 1.40e-02 5.10e+03 1.19e+00 bond pdb=" CB ARG L 18 " pdb=" CG ARG L 18 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.21e-01 ... (remaining 3440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 4515 1.65 - 3.30: 136 3.30 - 4.95: 31 4.95 - 6.60: 2 6.60 - 8.25: 2 Bond angle restraints: 4686 Sorted by residual: angle pdb=" C ASN E 331 " pdb=" N ILE E 332 " pdb=" CA ILE E 332 " ideal model delta sigma weight residual 121.70 129.09 -7.39 1.80e+00 3.09e-01 1.68e+01 angle pdb=" CA CYS E 432 " pdb=" CB CYS E 432 " pdb=" SG CYS E 432 " ideal model delta sigma weight residual 114.40 122.65 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" C LYS E 378 " pdb=" N CYS E 379 " pdb=" CA CYS E 379 " ideal model delta sigma weight residual 122.73 117.86 4.87 1.62e+00 3.81e-01 9.02e+00 angle pdb=" CA ASN E 331 " pdb=" C ASN E 331 " pdb=" N ILE E 332 " ideal model delta sigma weight residual 117.07 120.32 -3.25 1.21e+00 6.83e-01 7.22e+00 angle pdb=" C ASN L 94 " pdb=" N SER L 95 " pdb=" CA SER L 95 " ideal model delta sigma weight residual 121.80 128.12 -6.32 2.44e+00 1.68e-01 6.72e+00 ... (remaining 4681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 1822 17.59 - 35.17: 191 35.17 - 52.76: 28 52.76 - 70.34: 2 70.34 - 87.93: 3 Dihedral angle restraints: 2046 sinusoidal: 796 harmonic: 1250 Sorted by residual: dihedral pdb=" CA SER H 103 " pdb=" C SER H 103 " pdb=" N GLU H 104 " pdb=" CA GLU H 104 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 141.50 -48.50 1 1.00e+01 1.00e-02 3.24e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 135.33 -42.33 1 1.00e+01 1.00e-02 2.50e+01 ... (remaining 2043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 298 0.032 - 0.063: 135 0.063 - 0.094: 42 0.094 - 0.126: 29 0.126 - 0.157: 5 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA ILE E 332 " pdb=" N ILE E 332 " pdb=" C ILE E 332 " pdb=" CB ILE E 332 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA PRO L 81 " pdb=" N PRO L 81 " pdb=" C PRO L 81 " pdb=" CB PRO L 81 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 506 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU L 80 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO L 81 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO L 81 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 81 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO H 14 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 99 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO H 100 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " 0.023 5.00e-02 4.00e+02 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 966 2.81 - 3.33: 2748 3.33 - 3.85: 4865 3.85 - 4.38: 5494 4.38 - 4.90: 10028 Nonbonded interactions: 24101 Sorted by model distance: nonbonded pdb=" OG SER L 12 " pdb=" O VAL L 107 " model vdw 2.285 3.040 nonbonded pdb=" O SER H 86 " pdb=" NH1 ARG H 88 " model vdw 2.305 3.120 nonbonded pdb=" NH1 ARG E 457 " pdb=" O SER E 459 " model vdw 2.316 3.120 nonbonded pdb=" NH2 ARG L 55 " pdb=" O ILE L 59 " model vdw 2.355 3.120 nonbonded pdb=" NH2 ARG E 493 " pdb=" O GLY H 55 " model vdw 2.376 3.120 ... (remaining 24096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3445 Z= 0.189 Angle : 0.700 8.254 4686 Z= 0.371 Chirality : 0.046 0.157 509 Planarity : 0.005 0.056 605 Dihedral : 13.749 87.928 1227 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.40), residues: 425 helix: -3.48 (0.82), residues: 27 sheet: 0.31 (0.45), residues: 141 loop : -1.72 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 48 HIS 0.001 0.001 HIS E 505 PHE 0.011 0.002 PHE E 515 TYR 0.014 0.001 TYR E 453 ARG 0.004 0.000 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.292 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2176 time to fit residues: 17.5708 Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3445 Z= 0.299 Angle : 0.736 8.320 4686 Z= 0.384 Chirality : 0.048 0.166 509 Planarity : 0.006 0.065 605 Dihedral : 5.457 27.983 475 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.18 % Allowed : 10.35 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.40), residues: 425 helix: -3.25 (0.75), residues: 34 sheet: 0.46 (0.45), residues: 137 loop : -1.74 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 48 HIS 0.003 0.002 HIS E 505 PHE 0.019 0.002 PHE E 490 TYR 0.026 0.002 TYR E 453 ARG 0.003 0.000 ARG H 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.320 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.2456 time to fit residues: 17.1769 Evaluate side-chains 55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 21 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3445 Z= 0.229 Angle : 0.673 7.987 4686 Z= 0.350 Chirality : 0.045 0.167 509 Planarity : 0.005 0.067 605 Dihedral : 5.205 27.566 475 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.45 % Allowed : 13.62 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.40), residues: 425 helix: -3.23 (0.71), residues: 34 sheet: 0.55 (0.45), residues: 137 loop : -1.71 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 48 HIS 0.003 0.001 HIS E 505 PHE 0.012 0.002 PHE E 490 TYR 0.018 0.001 TYR E 453 ARG 0.003 0.000 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.296 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 0.2124 time to fit residues: 14.9200 Evaluate side-chains 58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3445 Z= 0.244 Angle : 0.678 8.211 4686 Z= 0.352 Chirality : 0.046 0.159 509 Planarity : 0.005 0.068 605 Dihedral : 5.135 26.900 475 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.63 % Allowed : 15.26 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.39), residues: 425 helix: -3.26 (0.69), residues: 34 sheet: 0.59 (0.44), residues: 137 loop : -1.71 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 48 HIS 0.002 0.001 HIS E 505 PHE 0.012 0.002 PHE E 490 TYR 0.018 0.002 TYR E 453 ARG 0.003 0.000 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.7013 (tmm-80) outliers start: 17 outliers final: 7 residues processed: 69 average time/residue: 0.2157 time to fit residues: 17.3902 Evaluate side-chains 60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.0010 chunk 23 optimal weight: 0.9990 overall best weight: 0.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3445 Z= 0.222 Angle : 0.653 7.813 4686 Z= 0.341 Chirality : 0.045 0.155 509 Planarity : 0.005 0.069 605 Dihedral : 5.112 26.333 475 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.27 % Allowed : 17.17 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.39), residues: 425 helix: -3.50 (0.69), residues: 33 sheet: 0.69 (0.45), residues: 137 loop : -1.64 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 48 HIS 0.002 0.001 HIS E 505 PHE 0.010 0.001 PHE H 27 TYR 0.015 0.001 TYR E 453 ARG 0.003 0.000 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7305 (ttp-110) cc_final: 0.7035 (tmm-80) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.2074 time to fit residues: 16.0339 Evaluate side-chains 60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3445 Z= 0.221 Angle : 0.652 7.724 4686 Z= 0.340 Chirality : 0.045 0.149 509 Planarity : 0.005 0.069 605 Dihedral : 5.038 26.024 475 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.36 % Allowed : 16.62 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.39), residues: 425 helix: -3.55 (0.68), residues: 33 sheet: 0.70 (0.45), residues: 137 loop : -1.64 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 436 HIS 0.002 0.001 HIS E 505 PHE 0.011 0.001 PHE H 27 TYR 0.014 0.001 TYR E 453 ARG 0.003 0.000 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7361 (ttp-110) cc_final: 0.7059 (tmm-80) outliers start: 16 outliers final: 12 residues processed: 68 average time/residue: 0.2030 time to fit residues: 16.5212 Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3445 Z= 0.231 Angle : 0.661 7.746 4686 Z= 0.345 Chirality : 0.045 0.145 509 Planarity : 0.005 0.068 605 Dihedral : 5.035 26.048 475 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.81 % Allowed : 17.98 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.39), residues: 425 helix: -3.45 (0.69), residues: 33 sheet: 0.69 (0.44), residues: 137 loop : -1.65 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 436 HIS 0.002 0.001 HIS E 505 PHE 0.016 0.002 PHE E 374 TYR 0.014 0.001 TYR E 453 ARG 0.003 0.000 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7401 (ttp-110) cc_final: 0.7080 (tmm-80) outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 0.2087 time to fit residues: 16.7238 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3445 Z= 0.239 Angle : 0.666 7.762 4686 Z= 0.348 Chirality : 0.045 0.151 509 Planarity : 0.005 0.073 605 Dihedral : 5.072 25.876 475 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.36 % Allowed : 17.44 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.39), residues: 425 helix: -3.40 (0.69), residues: 33 sheet: 0.68 (0.44), residues: 137 loop : -1.65 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 48 HIS 0.002 0.001 HIS E 505 PHE 0.017 0.002 PHE E 374 TYR 0.015 0.002 TYR H 81 ARG 0.003 0.000 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.487 Fit side-chains REVERT: L 18 ARG cc_start: 0.7417 (ttp-110) cc_final: 0.7077 (tmm-80) outliers start: 16 outliers final: 14 residues processed: 67 average time/residue: 0.1952 time to fit residues: 15.5674 Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3445 Z= 0.193 Angle : 0.659 7.429 4686 Z= 0.343 Chirality : 0.045 0.141 509 Planarity : 0.005 0.072 605 Dihedral : 5.031 26.459 475 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.09 % Allowed : 17.71 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.39), residues: 425 helix: -3.28 (0.71), residues: 33 sheet: 0.69 (0.44), residues: 142 loop : -1.56 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.002 0.001 HIS E 505 PHE 0.016 0.001 PHE E 374 TYR 0.010 0.001 TYR E 453 ARG 0.002 0.000 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.392 Fit side-chains REVERT: L 18 ARG cc_start: 0.7503 (ttp-110) cc_final: 0.7178 (tmm-80) REVERT: L 62 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7233 (ttm110) outliers start: 15 outliers final: 13 residues processed: 69 average time/residue: 0.2244 time to fit residues: 18.1206 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.0670 chunk 33 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3445 Z= 0.209 Angle : 0.666 7.532 4686 Z= 0.347 Chirality : 0.045 0.147 509 Planarity : 0.005 0.073 605 Dihedral : 5.030 26.215 475 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.81 % Allowed : 18.26 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.39), residues: 425 helix: -3.26 (0.72), residues: 33 sheet: 0.71 (0.44), residues: 142 loop : -1.50 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 48 HIS 0.002 0.001 HIS E 505 PHE 0.017 0.001 PHE E 374 TYR 0.012 0.001 TYR E 453 ARG 0.002 0.000 ARG E 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.386 Fit side-chains REVERT: L 18 ARG cc_start: 0.7507 (ttp-110) cc_final: 0.7189 (tmm-80) REVERT: L 62 ARG cc_start: 0.7537 (ttm110) cc_final: 0.7171 (ttm110) outliers start: 14 outliers final: 14 residues processed: 65 average time/residue: 0.2183 time to fit residues: 16.6585 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 15 optimal weight: 0.0980 chunk 41 optimal weight: 0.0050 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136276 restraints weight = 4266.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.140016 restraints weight = 2657.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142527 restraints weight = 1957.840| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3445 Z= 0.160 Angle : 0.625 6.818 4686 Z= 0.324 Chirality : 0.044 0.137 509 Planarity : 0.005 0.071 605 Dihedral : 4.785 26.150 475 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.00 % Allowed : 18.80 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.40), residues: 425 helix: -3.05 (0.75), residues: 33 sheet: 0.76 (0.44), residues: 142 loop : -1.36 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 48 HIS 0.001 0.001 HIS E 519 PHE 0.013 0.001 PHE E 374 TYR 0.008 0.001 TYR L 92 ARG 0.002 0.000 ARG H 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.03 seconds wall clock time: 25 minutes 23.83 seconds (1523.83 seconds total)